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Dear all,

I'm doing docking peptides to kinase structure by using flexpepdock. In the meanwhile I need ATP in the kinase structure, therefore I generated a param file for ATP. But after the prepack mode, the ATP has been removed from the pocket to the somewhere in the structure. Here is my question:

1) how should I fix the ATP in the pocket without any movement? Movemap or constrain file?

2)I was told to use movemap to fix the ATP. But I don't know how's the rosetta numbering of the HETATM. 

Hi everyone

Using placestub application, I want to place a set of stubs in target protein to use them for protein binder design. In this way, I want use 1000 scaffold (proteins to be substituted by appropriate stubs). Everything is OK with producing stubs, inverse rotamers, docking. But when I run placestub xml, it gives me this type of error in last line:

Hi,

I'd like to create a function in rosetta (in C++) that ultimately will accept a python dictionary when called from pyrosetta.  What's the best C++ class to use that will be the easiest for me to do the conversion from python dict?  (i.e. is there any existing pyrosetta code that will convert a python dictionary to, say, a C++ map).

Thanks in advance.

Hi,

i'm trying to dock a peptide into kinase. It's very important to keep ATP molecule in the kinase ortherwise some peptide simulation model will occupy ATP's position.

But the flexpepdock will remove all not aminoacid molecules. I was wondering is there any way I can do that ? Or an alternative module on Rosetta? 

Thank you!